Shadow Fleet is headed by the Fleet Commander, a Fleet Admiral, and the Fleet Executive Officer, an Admiral. These two officers oversee the running of the two major fleet commands:

The Operations & Support Command is tasked with managing the fleets organisation structure, comprising the Task Forces, Task Groups and individual SIMMs. It is headed by a Vice Admiral, with the senior Task Force Commander, a Rear Admiral, acting as his/her Executive Officer.

The Personnel & Training Command oversees all applications to Shadow Fleet and manages the Shadow Fleet Academy, fleet discipline, leaves of absence and recruitment. Again, this command is managed by a Vice Admiral, with a Rear Admiral as Executive Officer.

Shadow Fleet currently has three active shipboard roleplays, or "SIMMs", each with a full compliment of crew. The fleet also has one Earth Spacedock type Starbase, which is the Command and Control point for the fleet.